I'm a high school IT teacher, and can definitely relate to the lack of knowledge of the file system. It's particularly bad with students using a mac. We're now seeing a 50/50 split between win/mac and it seems that most kids are getting macs because that's the current fashion, but they really struggle with basic file ops. About 90% (no exaggeration) of mac students simply never discover the little down arrow that expands the file save dialog. This leads to students simply hitting save and having all their files dumped on the desktop. Then they minimize their app and move the recently saved file into another folder (usually also on desktop). Of course, in the case of a save as, this leads to a 'file deleted' message when they return to their program. Thus was a particular issue when I was teaching web dev and using vscode.
I try to teach file management in context where it makes sense. Web dev is a good topic to focus on it. Creating a folder to hold a site, sub folders for css,js,imgs and then relative file paths in html and css. These concepts are a first for many middle schoolers.
On the other hand kids are great at using virtual desktops on mac, whereas only maybe 2% of win users have discovered/use virtual desktops.